On my way to visit the Typas Lab at EMBL, Heidelberg for the next few months. Excited to chat about science. Ping me if you are in the area :)

This work would have been impossible without the contribution of my co-authors, the discussion from all JBD lab members, and the constant support from my advisor Joe Bondy-Denomy! Last, I am on the job market. Contact me if there are openings at your institutes! 16/16

Together, we discovered an immune system that specifically target phiKZ-like jumbophages. JukA is likely activated by ejected phage proteins, enabling cells to stop phages at early infection. Detection of ejected phage proteins represents a novel immune strategy. 15/n

3 of the novel immune systems consists of JukA homolog only, suggesting a single-component immune system. Fluorescence tagging shows that these three JukAs still serve as sensors by localizing to infection site upon infection (* labeled). 14/n

JukA is widespread and found next to various putative effectors. Is it possible JukA as a sensor has been recruited to other novel immune systems? Indeed, by testing 17 loci containing jukA homologs, we found 9 functional immune systems specifically target phiKZ. 13/n

Interestingly, JukA co-localize with ejected IB protein (gp90 shown, arrow) over the course of infection, but only co-localize with ejected phiKZ DNA in early infection (0&8 min). Thus, rather than ejected DNA, JukA likely senses ejected IB proteins. 12/n

Does JukA sense ejected proteins? In phage head, phiKZ genome is wrapped around a proteinaceous inner body (IB) structure. It is unclear if IB proteins are ejected with phiKZ genome. Via fluorescence tagging, Jingwen Guan showed that 4 IB proteins are ejected into host. 11/n

What does JukA sense? We inhibited cell translation and proved that JukA is not triggered by newly synthesized protein (A-D), but by ejected phiKZ factors. As JukA has no predicted DNA binding domain and cannot sense other phages, it’s unlikely that JukA senses phage DNA. 10/n

Is JukA or JukB responsible for sensing phiKZ infection? By testing JukA/B localization in the absence of each. We found this localization is dependent on JukA (C,D), suggesting JukA is the sensor of this two-compoent system. 9/n

Fluorescence tagging of Juk shows that: A) w/o phiKZ, JukA is diffuse while JukB forms motile puncta in cells, however, B) w/ phiKZ, JukA&B are rapidly recruited to the infection pole. 8/n

With limited info, we resorted to microscopy to study Juk mechanisms: with jukAB, A) phiKZ infection is neutralized before nucleus formation, and B) ejected phiKZ genome disappears. qPCR & RT-qPCR also confirms phiKZ DNA and RNA decreases with jukAB. Thus, Juk acts early. 7/n

A novel immune strategy? W/ help of Drs. Koonin and Makarova, we found JukA distributes broadly among bacteria but JukB doesnt. Neither has obvious functional domains. We further proved that Juk doesn’t prevent phage absorption, cleave phage DNA, or induce abortive infection. 6/n

By conducting a genome-wide screen with phiKZ-resistant isolate PA14, I found that disruption of two genes (jukA & jukB) sensitizes PA14 to phiKZ infection. Furthermore, expression of jukAB converts the sensitive isolate PAO1 to a resistant isolate against phiKZ. 5/n

Have bacteria evolved immune systems targeting the unique virology of phiKZ? By infecting a panel of Pseudomonas aeruginosa isolates, I noticed half of the isolates are resistant to phiKZ, suggesting the existence of phiKZ targeting immune system. 4/n

Senen found phiKZ anti-defense derives from a nucleus-like structure phiKZ assembles during infection. This nucleus, characterized by Pogliano lab at UCSD, houses phiKZ replication&transcription and prevents immune proteins from accessing phiKZ genomes (Mendoza, 2019,Nature). 3/n

The interest for such an immune system started as Senén Mendoza, a Bondy-Denomy lab alumni, discovered jumbophage phiKZ having the most potent anti-defense capability described to date, resisting all assayed DNA-targeting CRIPSR and R-M systems. 2/n

I showed Darwin’s finch specimens in Evolution today and the room became electrified! Notice the differences in beak shape and size, which is the essence of this adaptive radiation. ❤️ 🐦 🧬 ¡Viva La Evolución!